Share

Search Java Classes and Packages

Search Java Frameworks and Libraries

255581 classes and counting ...
Search Tips Index Status



# Classes and Interfaces in #HtsJDK - 489 results found.
NameDescriptionTypePackageFrameworkJavaDoc
AbstractAsyncWriterAbstract class that is designed to be extended and specialized to provide an asynchronous wrapper around any kind of Writer class that takes an object and writes it out somehow.Classhtsjdk.samtools.utilHtsJDKjavadoc
AbstractBAMFileIndexProvides basic, generic capabilities to be used reading BAM index files.Classhtsjdk.samtoolsHtsJDKjavadoc
AbstractBitCodecClasshtsjdk.samtools.cram.encodingHtsJDKjavadoc
AbstractFeatureCodecSimple basic class providing much of the basic functionality of codecs Every concrete subclass must implement FeatureCodec.Classhtsjdk.tribbleHtsJDKjavadoc
AbstractFeatureReader the feature reader class, which uses indices and codecs to read in Tribble file formats.Classhtsjdk.tribbleHtsJDKjavadoc
AbstractIndex An abstract implementation of the index class.Classhtsjdk.tribble.indexHtsJDKjavadoc
AbstractIteratorBase class of implementing iterators.Classhtsjdk.samtools.utilHtsJDKjavadoc
AbstractJavascriptFilterJavascript filter with HEADER type containing TYPE records.Classhtsjdk.samtools.filterHtsJDKjavadoc
AbstractProgressLoggerAbstract implementation of a Little progress logging class to facilitate consistent output of useful information when progressing through a stream of SAM records.Classhtsjdk.samtools.utilHtsJDKjavadoc
AbstractReaderClasshtsjdk.samtools.cram.encoding.readerHtsJDKjavadoc
AbstractSAMHeaderRecordBase class for the various concrete records in a SAM header, providing uniform access to the attributes.Classhtsjdk.samtoolsHtsJDKjavadoc
AbstractVCFCodecClasshtsjdk.variant.vcfHtsJDKjavadoc
AggregateFilterClasshtsjdk.samtools.filterHtsJDKjavadoc
AlignedFilterClasshtsjdk.samtools.filterHtsJDKjavadoc
AlignmentBlockRepresents the contiguous alignment of a subset of read bases to a reference sequence.Classhtsjdk.samtoolsHtsJDKjavadoc
AlignmentSpanA span of reads on a single reference.Classhtsjdk.samtools.cram.structureHtsJDKjavadoc
AlleleImmutable representation of an allele.Classhtsjdk.variant.variantcontextHtsJDKjavadoc
AsciiFeatureCodecA convenience base class for codecs that want to read in features from ASCII lines.Classhtsjdk.tribbleHtsJDKjavadoc
AsciiLineReaderA simple class that provides readLine() functionality around a PositionalBufferedStream BufferedReader and its BufferedReader.Classhtsjdk.tribble.readersHtsJDKjavadoc
AsciiLineReaderIteratorA class that iterates over the lines and line positions in an AsciiLineReader.Classhtsjdk.tribble.readersHtsJDKjavadoc
AsciiWriterFast (I hope) buffered Writer that converts char to byte merely by casting, rather than charset conversion.Classhtsjdk.samtools.utilHtsJDKjavadoc
AsyncFastqWriterClasshtsjdk.samtools.fastqHtsJDKjavadoc
AsynchronousLineReaderA LineReader implementation that delegates the work of reading and fetching lines to another thread.Classhtsjdk.tribble.readersHtsJDKjavadoc
AsyncVariantContextWriterAsyncVariantContextWriter that can be wrapped around an underlying AsyncVariantContextWriter to provide asynchronous output.Classhtsjdk.variant.variantcontext.writerHtsJDKjavadoc

Subscribe to Java News and Posts. Get latest updates and posts on Java from Buggybread.com
Enter your email address:
Delivered by FeedBurner

BamFileIoUtilsClasshtsjdk.samtoolsHtsJDKjavadoc
BAMFileSpanAn ordered list of chunks, capable of representing a set of discontiguous regions in the BAM file.Classhtsjdk.samtoolsHtsJDKjavadoc
BAMIndexA basic interface for querying BAM indices.Interfacehtsjdk.samtoolsHtsJDKjavadoc
BAMIndexerClass for both constructing BAM index content and writing it out.Classhtsjdk.samtoolsHtsJDKjavadoc
BAMIndexMetaDataMetadata about the bam index contained within the bam index.Classhtsjdk.samtoolsHtsJDKjavadoc
BamIndexValidatorClass to validate (at two different levels of thoroughness) the index for a BAM file.Classhtsjdk.samtoolsHtsJDKjavadoc
BAMRecordWrapper class for binary BAM records.Classhtsjdk.samtoolsHtsJDKjavadoc
BAMRecordCodecClass for translating between in-memory and disk representation of BAMRecord.Classhtsjdk.samtoolsHtsJDKjavadoc
BaseCategoryClasshtsjdk.samtools.cram.lossyHtsJDKjavadoc
BaseCategoryTypeenum BaseCategoryTypeEnum Constant SummaryClasshtsjdk.samtools.cram.lossyHtsJDKjavadoc
BaseQualityScoreA read feature representing a single quality score in a read.Classhtsjdk.samtools.cram.encoding.readfeaturesHtsJDKjavadoc
BasesClasshtsjdk.samtools.cram.encoding.readfeaturesHtsJDKjavadoc
BasicFastqWriterIn general FastqWriterFactory should be used so that AsyncFastqWriter can be enabled, but there are some cases in which that behavior is explicitly not wanted.Classhtsjdk.samtools.fastqHtsJDKjavadoc
BCF2CodecClasshtsjdk.variant.bcf2HtsJDKjavadoc
BCF2DecoderClasshtsjdk.variant.bcf2HtsJDKjavadoc
BCF2EncoderSee #BCFWriter for documentation on this classes role in encoding BCF2 filesSince:06/12Author:Mark DePristoClasshtsjdk.variant.variantcontext.writerHtsJDKjavadoc
BCF2FieldEncoderSee #BCFWriter for documentation on this classes role in encoding BCF2 filesSince:06/12Author:Mark DePristoClasshtsjdk.variant.variantcontext.writerHtsJDKjavadoc
BCF2FieldWriterSee #BCFWriter for documentation on this classes role in encoding BCF2 filesSince:06/12Author:Mark DePristoClasshtsjdk.variant.variantcontext.writerHtsJDKjavadoc
BCF2FieldWriterManagerSee #BCFWriter for documentation on this classes role in encoding BCF2 filesSince:06/12Author:Mark DePristoClasshtsjdk.variant.variantcontext.writerHtsJDKjavadoc
BCF2GenotypeFieldDecodersAn efficient scheme for building and obtaining specialized genotype field decoders.Classhtsjdk.variant.bcf2HtsJDKjavadoc
BCF2LazyGenotypesDecoderLazy version of genotypes decoder for BCF2 genotypesSince:5/12Author:Mark DePristoClasshtsjdk.variant.bcf2HtsJDKjavadoc
BCF2TypeBCF2 types and associated informationSince:05/12Author:depristoClasshtsjdk.variant.bcf2HtsJDKjavadoc
BCF2UtilsCommon utilities for working with BCF2 files Includes convenience methods for encoding, decoding BCF2 type descriptors (size + type)Classhtsjdk.variant.bcf2HtsJDKjavadoc
BCFVersionClasshtsjdk.variant.bcf2HtsJDKjavadoc
BEDCodecCodec for parsing BED file, as described by UCSC See https://genome.Classhtsjdk.tribble.bedHtsJDKjavadoc

Subscribe to Java News and Posts. Get latest updates and posts on Java from Buggybread.com
Enter your email address:
Delivered by FeedBurner

BEDFeatureInterfacehtsjdk.tribble.bedHtsJDKjavadoc
BetaIntegerEncodingClasshtsjdk.samtools.cram.encodingHtsJDKjavadoc
BinAn individual bin in a BAM file.Classhtsjdk.samtoolsHtsJDKjavadoc
BinaryCodecEncapsulates file representation of various primitive data types.Classhtsjdk.samtools.utilHtsJDKjavadoc
BinaryFeatureCodecClasshtsjdk.tribbleHtsJDKjavadoc
BinaryTagCodecConverter between disk and in-memory representation of a SAMRecord tag.Classhtsjdk.samtoolsHtsJDKjavadoc
BinListProvides a list of all bins which could exist in the BAM file.Classhtsjdk.samtoolsHtsJDKjavadoc
BinningIndexBuilderBuilder for a BinningIndexContent object.Classhtsjdk.samtoolsHtsJDKjavadoc
BinningIndexContentIn-memory representation of the binning index for a single reference.Classhtsjdk.samtoolsHtsJDKjavadoc
BitCodecAn interface that defines requirements for serializing/deserializing objects into and from a bit stream.Interfacehtsjdk.samtools.cram.encodingHtsJDKjavadoc
BitInputStreamAn interface to describe the requirements for reading bit data as opposed to bytes.Interfacehtsjdk.samtools.cram.ioHtsJDKjavadoc
BitOutputStreamAn interface to describe the requirements for writing out bits as opposed to bytes.Interfacehtsjdk.samtools.cram.ioHtsJDKjavadoc
BlockClass representing CRAM block concept and some methods to operate with block content.Classhtsjdk.samtools.cram.structureHtsJDKjavadoc
BlockClasshtsjdk.tribble.indexHtsJDKjavadoc
BlockCompressedFilePointerUtilStatic for manipulating virtual file pointers in BGZF files.Classhtsjdk.samtools.utilHtsJDKjavadoc
Check Code Snippets / Samples for htsjdk.samtools.util.BlockCompressedFilePointerUtil
BlockCompressedInputStreamClasshtsjdk.samtools.utilHtsJDKjavadoc
BlockCompressedOutputStreamWriter for a file that is a series of gzip blocks (BGZF format).Classhtsjdk.samtools.utilHtsJDKjavadoc
BlockCompressedStreamConstantsClasshtsjdk.samtools.utilHtsJDKjavadoc
BlockCompressionMethodenum BlockCompressionMethodEnum Constant SummaryClasshtsjdk.samtools.cram.structureHtsJDKjavadoc
BlockContentTypeenum BlockContentTypeEnum Constant SummaryClasshtsjdk.samtools.cram.structureHtsJDKjavadoc
BlockGunzipperAlternative to GZIPInputStream, for decompressing GZIP blocks that are already loaded into a byte[].Classhtsjdk.samtools.utilHtsJDKjavadoc
BrowseableBAMIndexAn index interface with additional functionality for querying and inspecting the structure of a BAM index.Interfacehtsjdk.samtoolsHtsJDKjavadoc
BufferedLineReader than AsciiLineReaderImpl.Classhtsjdk.samtools.utilHtsJDKjavadoc
ByteArrayLenEncodingClasshtsjdk.samtools.cram.encodingHtsJDKjavadoc
ByteArraySeekableStreamCreated by vadim on 23/03/2015.Classhtsjdk.samtools.seekablestreamHtsJDKjavadoc

Subscribe to Java News and Posts. Get latest updates and posts on Java from Buggybread.com
Enter your email address:
Delivered by FeedBurner

ByteArrayStopEncodingClasshtsjdk.samtools.cram.encodingHtsJDKjavadoc
ChrIndexInterfacehtsjdk.tribble.indexHtsJDKjavadoc
ChunkA [start,stop) file pointer pairing into the BAM file, stored as a BAM file index.Classhtsjdk.samtoolsHtsJDKjavadoc
CigarA list of CigarElements, which describes how a read aligns with the reference.Classhtsjdk.samtoolsHtsJDKjavadoc
CigarElementOne component of a cigar string.Classhtsjdk.samtoolsHtsJDKjavadoc
CigarOperatorThe operators that can appear in a cigar string, and information about their disk representations.Classhtsjdk.samtoolsHtsJDKjavadoc
CigarUtilClasshtsjdk.samtools.utilHtsJDKjavadoc
CloseableIteratorThis interface is used by iterators that use releasable resources during iteration.Interfacehtsjdk.samtools.utilHtsJDKjavadoc
CloseableTribbleIteratorThe basic iterator we use in Tribble, which allows closing and basic iteration.Interfacehtsjdk.tribbleHtsJDKjavadoc
CloserUtilUtility to close things that implement Closeable WARNING: This should only be used for Closeable things open for read, because it ignores exceptions, andClasshtsjdk.samtools.utilHtsJDKjavadoc
CodecLineParsingException a generic exception we use if the codec has trouble parsing the line its givenAuthor:aaronSee Also:Serialized FormClasshtsjdk.tribble.exceptionHtsJDKjavadoc
CodeUtilMiscellaneous util methods that don't fit anywhere else.Classhtsjdk.samtools.utilHtsJDKjavadoc
CollectionUtilSmall utility methods for dealing with collection classes.Classhtsjdk.samtools.utilHtsJDKjavadoc
CommonInfoCommon utility routines for VariantContext and GenotypeAuthor:depristoSee Also:Serialized FormClasshtsjdk.variant.variantcontextHtsJDKjavadoc
ComparableTupleA simple extension of the Tuple class that, for comparable Types, allows comparing Tuples of non-null elements.Classhtsjdk.samtools.utilHtsJDKjavadoc
CompoundFilterA Predicate on VariantContexts that returns true when either all its sub-predicates are true, or none are false.Classhtsjdk.variant.variantcontext.filterHtsJDKjavadoc
CompressionHeaderClasshtsjdk.samtools.cram.structureHtsJDKjavadoc
CompressionHeaderFactoryA class responsible for decisions about which encodings to use for a given set of records.Classhtsjdk.samtools.cram.buildHtsJDKjavadoc
ContainerClasshtsjdk.samtools.cram.structureHtsJDKjavadoc
ContainerFactoryClasshtsjdk.samtools.cram.buildHtsJDKjavadoc
ContainerIOMethods to read and write CRAM containers.Classhtsjdk.samtools.cram.structureHtsJDKjavadoc
ContainerParserClasshtsjdk.samtools.cram.buildHtsJDKjavadoc
ContentDigestsClasshtsjdk.samtools.cram.digestHtsJDKjavadoc
CoordinateSortedPairInfoMapHolds info about a mate pair for use when processing a coordinate sorted file.Classhtsjdk.samtoolsHtsJDKjavadoc
CoordMathClasshtsjdk.samtools.utilHtsJDKjavadoc

Subscribe to Java News and Posts. Get latest updates and posts on Java from Buggybread.com
Enter your email address:
Delivered by FeedBurner

CoordSpanInputSteamAn input stream that wraps a SeekableStream to produce only bytes specified within coordinates.Classhtsjdk.samtools.utilHtsJDKjavadoc
CountingInputStreamAn input stream that counts the bytes read from it.Classhtsjdk.samtools.cram.ioHtsJDKjavadoc
CountRecordsAn example of how to index a feature file, and then count all the records in the file.Classhtsjdk.tribble.exampleHtsJDKjavadoc
CRAIEntryA class representing CRAI index entry: file and alignment offsets for each slice.Classhtsjdk.samtools.cramHtsJDKjavadoc
CRAIIndexA collection of static methods to read, write and convert CRAI index.Classhtsjdk.samtools.cramHtsJDKjavadoc
Cram2SamRecordFactoryClasshtsjdk.samtools.cram.buildHtsJDKjavadoc
CramArrayMethods to read and write CRAM array of integers data type.Classhtsjdk.samtools.cram.ioHtsJDKjavadoc
CramCompressionRecordClasshtsjdk.samtools.cram.structureHtsJDKjavadoc
CramContainerIteratorAn iterator of CRAM containers read from an InputStream.Classhtsjdk.samtools.cram.buildHtsJDKjavadoc
CRAMContainerStreamWriterClass for writing SAMRecords into a series of CRAM containers on an output stream.Classhtsjdk.samtoolsHtsJDKjavadoc
CRAMExceptionCreated by edwardk on 8/13/15.Classhtsjdk.samtools.cramHtsJDKjavadoc
CRAMFileReaderBAMFileReader analogue for CRAM files.Classhtsjdk.samtoolsHtsJDKjavadoc
CRAMFileWriterClasshtsjdk.samtoolsHtsJDKjavadoc
CramHeaderA starting object when dealing with CRAM files.Classhtsjdk.samtools.cram.structureHtsJDKjavadoc
CRAMIndexerClass for both constructing BAM index content and writing it out.Classhtsjdk.samtoolsHtsJDKjavadoc
CramIntMethods to read and write CRAM int values as given in the file format specification.Classhtsjdk.samtools.cram.ioHtsJDKjavadoc
CramIOA collection of methods to open and close CRAM files.Classhtsjdk.samtools.cram.buildHtsJDKjavadoc
CRAMIteratorClasshtsjdk.samtoolsHtsJDKjavadoc
CramNormalizerClasshtsjdk.samtools.cram.buildHtsJDKjavadoc
CramRecordReaderClasshtsjdk.samtools.cram.encoding.readerHtsJDKjavadoc
CramSpanContainerIteratorAn iterator of CRAM containers read from locations in SeekableStream.Classhtsjdk.samtools.cram.buildHtsJDKjavadoc
CramVersionPoliciesThe class provides version-dependant rules and policies for CRAM data.Classhtsjdk.samtools.cram.commonHtsJDKjavadoc
CramVersionsClasshtsjdk.samtools.cram.commonHtsJDKjavadoc
CRC32InputStreamAn input stream that calculates CRC32 of all the bytes passed through it.Classhtsjdk.samtools.cram.ioHtsJDKjavadoc
CRC32OutputStreamAn output stream that calculates CRC32 checksum of all the bytes written through the stream.Classhtsjdk.samtools.cram.ioHtsJDKjavadoc

Subscribe to Java News and Posts. Get latest updates and posts on Java from Buggybread.com
Enter your email address:
Delivered by FeedBurner

CustomReaderFactoryFactory for creating custom readers for accessing API based resources, The configuration is controlled via custom_reader property (@see Defaults).Classhtsjdk.samtoolsHtsJDKjavadoc
DataReaderA basic interface for reading data.Interfacehtsjdk.samtools.cram.encoding.readerHtsJDKjavadoc
DataReaderFactoryClasshtsjdk.samtools.cram.encoding.readerHtsJDKjavadoc
DataSeriesAn annotation to denote a data series field in a java class.Classhtsjdk.samtools.cram.encodingHtsJDKjavadoc
DataSeriesMapClasshtsjdk.samtools.cram.encodingHtsJDKjavadoc
DataSeriesTypeData series types known to CRAM.Classhtsjdk.samtools.cram.encodingHtsJDKjavadoc
DataWriterA basic interface defining a writer.Interfacehtsjdk.samtools.cram.encoding.writerHtsJDKjavadoc
DataWriterFactoryClasshtsjdk.samtools.cram.encoding.writerHtsJDKjavadoc
DateParserNOTE: This code has been taken from w3.Classhtsjdk.samtools.utilHtsJDKjavadoc
DefaultBitInputStreamClasshtsjdk.samtools.cram.ioHtsJDKjavadoc
DefaultBitOutputStreamClasshtsjdk.samtools.cram.ioHtsJDKjavadoc
DefaultsEmbodies defaults for global values that affect how the SAM JDK operates.Classhtsjdk.samtoolsHtsJDKjavadoc
DefaultSAMRecordFactoryDefault factory for creating SAM and BAM records used by the SAMFileReader classes.Classhtsjdk.samtoolsHtsJDKjavadoc
DeflaterFactoryCreate zlib-based Deflater if JNI library and other require libraries are available, otherwise create standard Java 7 has its own Deflater implementation (libzip.Classhtsjdk.samtools.util.zipHtsJDKjavadoc
DelegatingIteratorSimple iterator class that delegates all method calls to an underlying iterator.Classhtsjdk.samtools.utilHtsJDKjavadoc
DeletionA read feature representing a deletion of one or more bases similar to CigarOperator.Classhtsjdk.samtools.cram.encoding.readfeaturesHtsJDKjavadoc
DiploidGenotypeenum DiploidGenotype Enum describing all possible combinations of diploid genotype variations;Classhtsjdk.tribble.gelitextHtsJDKjavadoc
DiskBackedQueueA single-ended FIFO queue.Classhtsjdk.samtools.utilHtsJDKjavadoc
DiskBasedBAMFileIndexA class for reading BAM file indices, hitting the disk once per query.Classhtsjdk.samtoolsHtsJDKjavadoc
DownsamplingIteratorAbstract base class for all DownsamplingIterators that provides a uniform interface for recording and reporting statistics bout how many records have been kept and discarded.Classhtsjdk.samtoolsHtsJDKjavadoc
DownsamplingIteratorFactoryA factory for creating DownsamplingIterators that uses a number of different strategies to achieve downsampling while meeting various criteria.Classhtsjdk.samtoolsHtsJDKjavadoc
DuplicateReadFilterClasshtsjdk.samtools.filterHtsJDKjavadoc
DuplicateScoringStrategyThis class helps us compute and compare duplicate scores, which are used for selecting the non-duplicate during duplicate marking (see MarkDuplicates).Classhtsjdk.samtoolsHtsJDKjavadoc
DuplicateSetStores a set of records that are duplicates of each other.Classhtsjdk.samtoolsHtsJDKjavadoc
DuplicateSetIteratorAn iterator of sets of duplicates.Classhtsjdk.samtoolsHtsJDKjavadoc

Subscribe to Java News and Posts. Get latest updates and posts on Java from Buggybread.com
Enter your email address:
Delivered by FeedBurner

DynamicIndexCreatorA DynamicIndexCreator creates the proper index based on an IndexFactory.Classhtsjdk.tribble.indexHtsJDKjavadoc
EnaRefServiceClasshtsjdk.samtools.cram.refHtsJDKjavadoc
EncodingAn interface to describe how a data series is encoded.Interfacehtsjdk.samtools.cram.encodingHtsJDKjavadoc
EncodingFactoryA helper class to instantiate an appropriate Encoding for a given DataSeriesType andClasshtsjdk.samtools.cram.encodingHtsJDKjavadoc
EncodingIDEncoding ID as defined in the CRAM specs.Classhtsjdk.samtools.cram.structureHtsJDKjavadoc
EncodingKeyClasshtsjdk.samtools.cram.structureHtsJDKjavadoc
EncodingParamsClasshtsjdk.samtools.cram.structureHtsJDKjavadoc
ExampleBinaryCodecAn example binary codec that encodes / decodes contig / start / stop values via DataInputStreamsAuthor:Mark DePristoClasshtsjdk.tribble.exampleHtsJDKjavadoc
ExampleSamUsageClasshtsjdk.samtools.exampleHtsJDKjavadoc
ExposedByteArrayOutputStreamClasshtsjdk.samtools.cram.ioHtsJDKjavadoc
ExternalByteArrayEncodingClasshtsjdk.samtools.cram.encodingHtsJDKjavadoc
ExternalByteEncodingClasshtsjdk.samtools.cram.encodingHtsJDKjavadoc
ExternalCompressionMethods to provide CRAM external compression/decompression features.Classhtsjdk.samtools.cram.ioHtsJDKjavadoc
ExternalCompressorClasshtsjdk.samtools.cram.encodingHtsJDKjavadoc
ExternalIntegerEncodingClasshtsjdk.samtools.cram.encodingHtsJDKjavadoc
ExternalLongEncodingClasshtsjdk.samtools.cram.encodingHtsJDKjavadoc
FailsVendorReadQualityFilterClasshtsjdk.samtools.filterHtsJDKjavadoc
FastaSequenceFileClasshtsjdk.samtools.referenceHtsJDKjavadoc
FastaSequenceIndexReads a fasta index file (.Classhtsjdk.samtools.referenceHtsJDKjavadoc
FastGenotypeThis class encompasses all the basic information about a genotype.Classhtsjdk.variant.variantcontextHtsJDKjavadoc
FastLineReaderLine-oriented InputStream reader that uses one buffer for disk buffering and line-termination-finding, in order to improve performance.Classhtsjdk.samtools.utilHtsJDKjavadoc
FastqConstantsClasshtsjdk.samtools.fastqHtsJDKjavadoc
FastqQualityFormatenum FastqQualityFormatEnumeration for FastQ quality score formats formats.Classhtsjdk.samtools.utilHtsJDKjavadoc
FastqReaderReads a FASTQ file with four lines per record.Classhtsjdk.samtools.fastqHtsJDKjavadoc
FastqRecordRepresents a fastq record, fairly literally, i.Classhtsjdk.samtools.fastqHtsJDKjavadoc

Subscribe to Java News and Posts. Get latest updates and posts on Java from Buggybread.com
Enter your email address:
Delivered by FeedBurner

FastqWriterSimple interface for a class that can write out fastq records.Interfacehtsjdk.samtools.fastqHtsJDKjavadoc
FastqWriterFactoryFactory class for creating FastqWriter objects.Classhtsjdk.samtools.fastqHtsJDKjavadoc
FeatureRepresents a locus on a reference sequence.Interfacehtsjdk.tribbleHtsJDKjavadoc
FeatureCodecThe base interface for classes that read in features.Interfacehtsjdk.tribbleHtsJDKjavadoc
FeatureCodecHeaderA class to represent a header of a feature containing file.Classhtsjdk.tribbleHtsJDKjavadoc
FeatureReaderthe basic interface that feature sources need to matchCloseableTribbleIterInterfacehtsjdk.tribbleHtsJDKjavadoc
FileAppendStreamLRUCacheLRU cache of OutputStreams to handle situation in which it is necessary to have more FileOutputStreams than resource limits will allow.Classhtsjdk.samtools.utilHtsJDKjavadoc
FileTruncatedExceptionThrown when it is possible to detect that a SAM or BAM file is truncated.Classhtsjdk.samtoolsHtsJDKjavadoc
FilteringIteratorFiltering Iterator which takes a filter and an iterator and iterates through only those records which are not rejected by the filter.Classhtsjdk.samtools.filterHtsJDKjavadoc
FilteringIteratorA filtering iterator for VariantContexts that takes a base iterator and a VariantContextFilter.Classhtsjdk.variant.variantcontext.filterHtsJDKjavadoc
FixBAMFileClasshtsjdk.samtoolsHtsJDKjavadoc
FormatUtilSimple class used to format object values into a standard format for printing.Classhtsjdk.samtools.utilHtsJDKjavadoc
FTPClientClasshtsjdk.samtools.util.ftpHtsJDKjavadoc
FTPHelperClasshtsjdk.tribble.utilHtsJDKjavadoc
FTPReplyClasshtsjdk.samtools.util.ftpHtsJDKjavadoc
FTPStreamA "non-seekable" ftp stream.Classhtsjdk.samtools.util.ftpHtsJDKjavadoc
FTPUtilsClasshtsjdk.samtools.util.ftpHtsJDKjavadoc
FullBEDFeatureObject for full BED file.Classhtsjdk.tribble.bedHtsJDKjavadoc
GammaIntegerEncodingClasshtsjdk.samtools.cram.encodingHtsJDKjavadoc
GeliTextCodec A codec for parsing geli text files, which is the text version of the geli binary format.Classhtsjdk.tribble.gelitextHtsJDKjavadoc
GeliTextFeature Class GeliTextFeature This is a feature for the Geli text object, which is the text version of the Geli binary genotyping format.Classhtsjdk.tribble.gelitextHtsJDKjavadoc
GeneralUtilsClasshtsjdk.variant.utilsHtsJDKjavadoc
GenomicIndexUtilClasshtsjdk.samtoolsHtsJDKjavadoc
GenotypeThis class encompasses all the basic information about a genotype.Classhtsjdk.variant.variantcontextHtsJDKjavadoc
GenotypeBuilderA builder class for genotypes Provides convenience setter methods for all of the Genotype fieldClasshtsjdk.variant.variantcontextHtsJDKjavadoc

Subscribe to Java News and Posts. Get latest updates and posts on Java from Buggybread.com
Enter your email address:
Delivered by FeedBurner

GenotypeLikelihoodsClasshtsjdk.variant.variantcontextHtsJDKjavadoc
GenotypeQualityFilterA Predicate on VariantContexts that returns true at sites that are either unfiltered, or passing (as variants).Classhtsjdk.variant.variantcontext.filterHtsJDKjavadoc
GenotypesContextRepresents an ordered collection of Genotype objectsSee Also:Serialized FormClasshtsjdk.variant.variantcontextHtsJDKjavadoc
GenotypeTypeSummary types for Genotype objectsSince:Date createdAuthor:Your NameClasshtsjdk.variant.variantcontextHtsJDKjavadoc
GolombIntegerEncodingClasshtsjdk.samtools.cram.encodingHtsJDKjavadoc
GolombLongEncodingClasshtsjdk.samtools.cram.encodingHtsJDKjavadoc
GolombRiceIntegerEncodingClasshtsjdk.samtools.cram.encodingHtsJDKjavadoc
HardClipA read feature representing a hard clip similar to CigarOperator.Classhtsjdk.samtools.cram.encoding.readfeaturesHtsJDKjavadoc
HardyWeinbergCalculationThis class calculates a HardyWeinberg p-value given three values representing the observed frequences of homozygous and heterozygous genotypes in theClasshtsjdk.tribble.util.popgenHtsJDKjavadoc
HeaderA header for a metrics file.Interfacehtsjdk.samtools.metricsHtsJDKjavadoc
HeterozygosityFilterA Predicate on VariantContexts that either returns true at heterozygous sites (invertible to false).Classhtsjdk.variant.variantcontext.filterHtsJDKjavadoc
HistogramClass for computing and accessing histogram type data.Classhtsjdk.samtools.utilHtsJDKjavadoc
HTTPHelperSimple implementation of URLHelper based on the JDK URL and HttpURLConnection classes.Classhtsjdk.tribble.utilHtsJDKjavadoc
HttpUtilsClasshtsjdk.samtools.utilHtsJDKjavadoc
HuffmanByteEncodingClasshtsjdk.samtools.cram.encoding.huffman.codecHtsJDKjavadoc
HuffmanCodeClasshtsjdk.samtools.cram.encoding.huffmanHtsJDKjavadoc
HuffmanIntegerEncodingClasshtsjdk.samtools.cram.encoding.huffman.codecHtsJDKjavadoc
HuffmanTreeClasshtsjdk.samtools.cram.encoding.huffmanHtsJDKjavadoc
IndexInterface for all index implementations.Classhtsjdk.tribble.indexHtsJDKjavadoc
IndexCreatorInterfacehtsjdk.tribble.indexHtsJDKjavadoc
IndexedFastaSequenceFileA fasta file driven by an index for fast, concurrent lookups.Classhtsjdk.samtools.referenceHtsJDKjavadoc
IndexFactoryFactory class for creating indexes.Classhtsjdk.tribble.indexHtsJDKjavadoc
IndexToTableClasshtsjdk.tribble.exampleHtsJDKjavadoc
IndicesAreEqualClasshtsjdk.tribble.exampleHtsJDKjavadoc
InputStreamUtilsConvenience methods to read from InputStream.Classhtsjdk.samtools.cram.ioHtsJDKjavadoc

Subscribe to Java News and Posts. Get latest updates and posts on Java from Buggybread.com
Enter your email address:
Delivered by FeedBurner

InsertBaseA read feature representing a single insert base.Classhtsjdk.samtools.cram.encoding.readfeaturesHtsJDKjavadoc
InsertionA read feature representing a multi-base insertion.Classhtsjdk.samtools.cram.encoding.readfeaturesHtsJDKjavadoc
InsertSizeFilterFilter things that fall outside a specified range of insert sizes.Classhtsjdk.samtools.filterHtsJDKjavadoc
IntelDeflaterThis is a copy of java.Classhtsjdk.samtools.util.zipHtsJDKjavadoc
IntervalRepresents a simple interval on a sequence.Classhtsjdk.samtools.utilHtsJDKjavadoc
IntervalQuick and dirty interval class Describes a genomic interval and where in a file information for thatClasshtsjdk.tribble.index.intervalHtsJDKjavadoc
IntervalFilterFilter SAMRecords so that only those that overlap the given list of intervals.Classhtsjdk.samtools.filterHtsJDKjavadoc
IntervalIndexCreatorClasshtsjdk.tribble.index.intervalHtsJDKjavadoc
IntervalListRepresents a list of intervals against a reference sequence that can be written to and read from a file.Classhtsjdk.samtools.utilHtsJDKjavadoc
IntervalListReferenceSequenceMaskServe up loci of interest based on an interval list.Classhtsjdk.samtools.utilHtsJDKjavadoc
IntervalTreeA Red-Black tree with intervals for keys.Classhtsjdk.samtools.utilHtsJDKjavadoc
IntervalTreeAn implementation of an interval tree, following the explanation.Classhtsjdk.tribble.index.intervalHtsJDKjavadoc
IntervalTreeIndexIndex based on an interval treeAuthor:jrobinsoSee Also:IntervalTreeClasshtsjdk.tribble.index.intervalHtsJDKjavadoc
IntervalTreeMapUtility class that implements an interval map.Classhtsjdk.samtools.utilHtsJDKjavadoc
IntervalUtilClasshtsjdk.samtools.utilHtsJDKjavadoc
IntGenotypeFieldAccessorsA convenient way to provide a single view on the many int and int[] field values we work with, for writing out the values.Classhtsjdk.variant.variantcontext.writerHtsJDKjavadoc
IntHashMap A hash map that uses primitive ints for the key rather than objects.Classhtsjdk.samtools.cram.commonHtsJDKjavadoc
IOUtilMiscellaneous stateless static IO-oriented methods.Classhtsjdk.samtools.utilHtsJDKjavadoc
ISeekableStreamFactoryFactory for creating SeekableStreams based on URLs/paths.Interfacehtsjdk.samtools.seekablestreamHtsJDKjavadoc
Iso8601DateUse this type rather than java.Classhtsjdk.samtools.utilHtsJDKjavadoc
IterableAdapterProvides an adapter to wrap an Iterator with an Iterable, allowing it to be run through a foreach loop.Classhtsjdk.samtools.utilHtsJDKjavadoc
IterableOnceIteratorAbstract implementation of an iterator that also implements Iterable (to return itself) so that it can be used if for() loops.Classhtsjdk.samtools.utilHtsJDKjavadoc
IterablesClasshtsjdk.samtools.utilHtsJDKjavadoc
ITF8Methods to read and write int values as per ITF8 specification in CRAM.Classhtsjdk.samtools.cram.ioHtsJDKjavadoc
JavascriptSamRecordFilterjavascript based read filter The script puts the following variables in the script context:Classhtsjdk.samtools.filterHtsJDKjavadoc

Subscribe to Java News and Posts. Get latest updates and posts on Java from Buggybread.com
Enter your email address:
Delivered by FeedBurner

JavascriptVariantFilterjavascript based variant filter The script puts the following variables in the script context:Classhtsjdk.variant.variantcontext.filterHtsJDKjavadoc
LazySimple utility for building an on-demand (lazy) object-initializer.Classhtsjdk.samtools.utilHtsJDKjavadoc
LazyGenotypesContextLazy-loading GenotypesContext.Classhtsjdk.variant.variantcontextHtsJDKjavadoc
LiftOverJava port of UCSC liftOver.Classhtsjdk.samtools.liftoverHtsJDKjavadoc
LinearIndexThe linear index associated with a given reference in a BAM index.Classhtsjdk.samtoolsHtsJDKjavadoc
LinearIndexIndex defined by dividing the genome by chromosome, then each chromosome into bins of fixed width (in genomic coordinates).Classhtsjdk.tribble.index.linearHtsJDKjavadoc
LinearIndexCreatorFor creating a LinearIndex from a stream of features.Classhtsjdk.tribble.index.linearHtsJDKjavadoc
LineIteratorA very simple descriptor for line-iterables.Interfacehtsjdk.tribble.readersHtsJDKjavadoc
LineIteratorImplA simple iterator over the elements in LineReader.Classhtsjdk.tribble.readersHtsJDKjavadoc
LineReaderInterface allows for implementations that read lines from a String, an ASCII file, or somewhere else.Interfacehtsjdk.samtools.utilHtsJDKjavadoc
LineReaderInterface for line-oriented readers.Interfacehtsjdk.tribble.readersHtsJDKjavadoc
LineReaderUtilA collection of factories for generating LineReaders.Classhtsjdk.tribble.readersHtsJDKjavadoc
ListMapA Map class that holds a list of entries under each key instead of a single entry, and provides utility methods for adding an entry under a key.Classhtsjdk.samtools.utilHtsJDKjavadoc
LittleEndianInputStreamInput stream with methods to convert byte arrays to numeric values using "little endian" order.Classhtsjdk.tribble.utilHtsJDKjavadoc
LittleEndianOutputStreamClasshtsjdk.tribble.utilHtsJDKjavadoc
LocatableAny class that has a single logical mapping onto the genome should implement Locatable positions should be reported as 1-based and closed at both endsInterfacehtsjdk.samtools.utilHtsJDKjavadoc
LocationAwareDescribes API for getting current position in a stream, writer, or underlying file.Interfacehtsjdk.samtools.utilHtsJDKjavadoc
LocusLocation info about a locus.Interfacehtsjdk.samtools.utilHtsJDKjavadoc
LocusComparatorcompares first by sequence index then by positionAuthor:Doug Voet (dvoet at broadinstitute dot org)See Also:Serialized FormClasshtsjdk.samtools.utilHtsJDKjavadoc
LocusImplSimple implementation of Locus interface for ease of passing as an arg and comparing with other Locus implementations.Classhtsjdk.samtools.utilHtsJDKjavadoc
LogA wafer thin wrapper around System.Classhtsjdk.samtools.utilHtsJDKjavadoc
LongLineBufferedReaderA variant of BufferedReader with improved performance reading files with long lines.Classhtsjdk.tribble.readersHtsJDKjavadoc
LTF8Methods to read and write LTF8 as per CRAM specs.Classhtsjdk.samtools.cram.ioHtsJDKjavadoc
MappingQualityFilterFilter things with low mapping quality.Classhtsjdk.samtools.filterHtsJDKjavadoc
MathUtilsClasshtsjdk.tribble.utilHtsJDKjavadoc

Subscribe to Java News and Posts. Get latest updates and posts on Java from Buggybread.com
Enter your email address:
Delivered by FeedBurner

Md5CalculatingInputStreamClass to generate an MD5 string for a file as it is being readAuthor:ktibbett@broadinstitue.Classhtsjdk.samtools.utilHtsJDKjavadoc
Md5CalculatingOutputStreamClass to generate an MD5 string for a file as it is being readAuthor:ktibbett@broadinstitue.Classhtsjdk.samtools.utilHtsJDKjavadoc
MergingIteratorAn iterator over Iterators that return Ts.Classhtsjdk.samtools.utilHtsJDKjavadoc
MergingSamRecordIteratorProvides an iterator interface for merging multiple underlying iterators into a single iterable stream.Classhtsjdk.samtoolsHtsJDKjavadoc
MetricBaseA base class from which all Metric classes should inherit.Classhtsjdk.samtools.metricsHtsJDKjavadoc
MetricsFileContains a set of metrics that can be written to a file and parsed back again.Classhtsjdk.samtools.metricsHtsJDKjavadoc
Murmur3Provides an implementation of the Murmur3_32 hash algorithm that has desirable properties in terms of randomness and uniformity of the distribution of output values that make it a useful hashing algorithm for downsampling.Classhtsjdk.samtools.utilHtsJDKjavadoc
MutableIndexSome Index implementations can be modified in memory.Interfacehtsjdk.tribble.indexHtsJDKjavadoc
MutableIntClasshtsjdk.samtools.cram.commonHtsJDKjavadoc
NameAwareCodecCreated by IntelliJ IDEA.Interfacehtsjdk.tribbleHtsJDKjavadoc
NotPrimaryAlignmentFilterClasshtsjdk.samtools.filterHtsJDKjavadoc
NotPrimarySkippingIteratorWrapper around SAMRecord iterator that skips over non-primary elements.Classhtsjdk.samtoolsHtsJDKjavadoc
NullEncodingClasshtsjdk.samtools.cram.encodingHtsJDKjavadoc
ObjectsSubset of JDK7's Objects for non-JDK7 support.Classhtsjdk.samtools.utilHtsJDKjavadoc
OptionsAvailable writer options for VariantContextWritersSince:5/12Author:Mark DePristoClasshtsjdk.variant.variantcontext.writerHtsJDKjavadoc
OverclippedReadFilterFilters out reads with very few unclipped bases, likely due to the read coming from a foreign organism, e.Classhtsjdk.samtools.filterHtsJDKjavadoc
OverlapDetectorUtility class to efficiently do in memory overlap detection between a large set of mapping like objects, and one or more candidate mappings.Classhtsjdk.samtools.utilHtsJDKjavadoc
PaddingA read feature representing padding, similar to CigarOperator.Classhtsjdk.samtools.cram.encoding.readfeaturesHtsJDKjavadoc
ParsingUtilsClasshtsjdk.tribble.utilHtsJDKjavadoc
PassingVariantFilterA Predicate on VariantContexts that returns true at sites that are either unfiltered, or passing (as variants).Classhtsjdk.variant.variantcontext.filterHtsJDKjavadoc
PeekableIteratorClasshtsjdk.samtools.utilHtsJDKjavadoc
PeekIteratorWrapper around an iterator that enables non-destructive peeking at the next element that would be returned by next()Classhtsjdk.samtools.utilHtsJDKjavadoc
PositionalMinimal interface for an object at support getting the current position in the stream / writer / file, as well as a handful of other reader-like features.Interfacehtsjdk.tribble.readersHtsJDKjavadoc
PositionalBufferedStreamA wrapper around an InputStream which performs it's own buffering, and keeps track of the position.Classhtsjdk.tribble.readersHtsJDKjavadoc
PreservationPolicyClasshtsjdk.samtools.cram.lossyHtsJDKjavadoc

Subscribe to Java News and Posts. Get latest updates and posts on Java from Buggybread.com
Enter your email address:
Delivered by FeedBurner

ProcessExecutorUtility class that will execute sub processes via Runtime.Classhtsjdk.samtools.utilHtsJDKjavadoc
ProfileIndexReadingClasshtsjdk.tribble.exampleHtsJDKjavadoc
ProgressLoggerLittle progress logging class to facilitate consistent output of useful information when progressing through a stream of SAM records.Classhtsjdk.samtools.utilHtsJDKjavadoc
ProgressLoggerInterfaceAn interface defining the record() methods of the Picard-public ProgressLogger implementation.Interfacehtsjdk.samtools.utilHtsJDKjavadoc
QualityEncodingDetectorUtility for determining the type of quality encoding/format (see FastqQualityFormat) used in a SAM/BAM or Fastq.Classhtsjdk.samtools.utilHtsJDKjavadoc
QualityScorePreservationClasshtsjdk.samtools.cram.lossyHtsJDKjavadoc
QualityScoreTreatmentClasshtsjdk.samtools.cram.lossyHtsJDKjavadoc
QualityScoreTreatmentTypeenum QualityScoreTreatmentTypeEnum Constant SummaryClasshtsjdk.samtools.cram.lossyHtsJDKjavadoc
QualityUtilUtility class for working with quality scores and error probabilities.Classhtsjdk.samtools.utilHtsJDKjavadoc
QueryIntervalInterval relative to a reference, for querying a BAM file.Classhtsjdk.samtoolsHtsJDKjavadoc
RANSClasshtsjdk.samtools.cram.encoding.ransHtsJDKjavadoc
ReadBaseA read feature representing a single base with associated quality score.Classhtsjdk.samtools.cram.encoding.readfeaturesHtsJDKjavadoc
ReadCategoryClasshtsjdk.samtools.cram.lossyHtsJDKjavadoc
ReadCategoryTypeenum ReadCategoryTypeEnum Constant SummaryClasshtsjdk.samtools.cram.lossyHtsJDKjavadoc
ReadFeatureAn interface to capture data in read coordinates.Interfacehtsjdk.samtools.cram.encoding.readfeaturesHtsJDKjavadoc
ReadNameFilterClasshtsjdk.samtools.filterHtsJDKjavadoc
ReadTagCRAM counterpart of SAMTag.Classhtsjdk.samtools.cram.structureHtsJDKjavadoc
ReferenceCacheThat is a thread-safe wrapper for a list of cache Reference objects.Classhtsjdk.samtools.sraHtsJDKjavadoc
ReferenceSequenceWrapper around a reference sequence that has been read from a reference file.Classhtsjdk.samtools.referenceHtsJDKjavadoc
ReferenceSequenceFileAn interface for working with files of reference sequences regardless of the file formatRetrieves the complete sequence described by this contig.Interfacehtsjdk.samtools.referenceHtsJDKjavadoc
ReferenceSequenceFileFactoryFactory class for creating ReferenceSequenceFile instances for reading reference sequences store in various formats.Classhtsjdk.samtools.referenceHtsJDKjavadoc
ReferenceSequenceFileWalkerManages a ReferenceSequenceFile.Classhtsjdk.samtools.referenceHtsJDKjavadoc
ReferenceSequenceMaskInterface for specifying loci of interest for genotype calling and other operations.Interfacehtsjdk.samtools.utilHtsJDKjavadoc
ReferenceSourceClasshtsjdk.samtools.cram.refHtsJDKjavadoc
ReferenceTracksClasshtsjdk.samtools.cram.refHtsJDKjavadoc

Subscribe to Java News and Posts. Get latest updates and posts on Java from Buggybread.com
Enter your email address:
Delivered by FeedBurner

RefSeqIdReaderA reader that only keeps track of alignment spans.Classhtsjdk.samtools.cram.encoding.readerHtsJDKjavadoc
RefSkipA read feature representing a reference skip similar to CigarOperator.Classhtsjdk.samtools.cram.encoding.readfeaturesHtsJDKjavadoc
RelativeIso8601DateLike Iso8601Date, but also comes in a "lazy now" flavor.Classhtsjdk.samtools.utilHtsJDKjavadoc
RemoteURLHelper Determines appropriate helper based on protocol (ftp/http), and then delegates.Classhtsjdk.tribble.utilHtsJDKjavadoc
ReservedTagConstantsClasshtsjdk.samtoolsHtsJDKjavadoc
ResourceLimitedMapLRU collection class for managing objects that place some resource burden such that not too many of them can existing in the VM at one time, but they can be reconstructed ias necessary.Classhtsjdk.samtools.utilHtsJDKjavadoc
ResourceLimitedMapFunctorc.Interfacehtsjdk.samtools.utilHtsJDKjavadoc
RuntimeEOFExceptionThrown by various codecs to indicate EOF without having to clutter the API with throws clausesSee Also:Serialized FormClasshtsjdk.samtools.utilHtsJDKjavadoc
RuntimeIOExceptionThrown by various IO classes to indicate IOException without having to clutter the API with throws clausesSee Also:Serialized FormClasshtsjdk.samtools.utilHtsJDKjavadoc
RuntimeScriptExceptionThrown by classes handling script engines like the javascript-based filters for SAM/VCFSee Also:Serialized FormClasshtsjdk.samtools.utilHtsJDKjavadoc
Sam2CramRecordFactoryClasshtsjdk.samtools.cram.buildHtsJDKjavadoc
SAMBinaryTagAndUnsignedArrayValueSimple extension to SAMBinaryTagAndValue in order to distinguish unsigned array values, because signedness cannot be determined by introspection of value.Classhtsjdk.samtoolsHtsJDKjavadoc
SAMBinaryTagAndValueHolds a SAMRecord attribute and the tagname (in binary form) for that attribute.Classhtsjdk.samtoolsHtsJDKjavadoc
SAMExceptionClasshtsjdk.samtoolsHtsJDKjavadoc
Check Code Snippets / Samples for htsjdk.samtools.SAMException
SAMFileHeaderHeader information from a SAM or BAM file.Classhtsjdk.samtoolsHtsJDKjavadoc
SamFileHeaderMergerMerges SAMFileHeaders that have the same sequences into a single merged header object while providing read group translation for cases where read groupsClasshtsjdk.samtoolsHtsJDKjavadoc
SAMFileReaderClass for reading and querying SAM/BAM files.Classhtsjdk.samtoolsHtsJDKjavadoc
SamFilesClasshtsjdk.samtoolsHtsJDKjavadoc
SAMFileSourceRepresents the origin of a SAM record.Classhtsjdk.samtoolsHtsJDKjavadoc
SAMFileSpanA interface representing a collection of (possibly) discontinuous segments in the BAM file, possibly representing the results of an index query.Interfacehtsjdk.samtoolsHtsJDKjavadoc
SAMFileTruncatedReaderA truncated form of a SAMFileReader that iterates over a limited number of records.Classhtsjdk.samtoolsHtsJDKjavadoc
SamFileValidatorValidates SAM files as follows: checks sam file header for sequence dictionarychecks sam file header for read groupsfor each sam recordClasshtsjdk.samtoolsHtsJDKjavadoc
SAMFileWriterInterface for SAMText and BAM file writers.Interfacehtsjdk.samtoolsHtsJDKjavadoc
SAMFileWriterFactoryCreate a writer for writing SAM, BAM, or CRAM files.Classhtsjdk.samtoolsHtsJDKjavadoc
SAMFileWriterImplBase class for implementing SAM writer with any underlying format.Classhtsjdk.samtoolsHtsJDKjavadoc

Subscribe to Java News and Posts. Get latest updates and posts on Java from Buggybread.com
Enter your email address:
Delivered by FeedBurner

SAMFlagSAM flags as enum, to be used in GUI, menu, etc.Classhtsjdk.samtoolsHtsJDKjavadoc
SAMFormatExceptionThrown when a SAM file being read or decoded (text or binary) looks bad.Classhtsjdk.samtoolsHtsJDKjavadoc
SAMHeaderRecordComparatorProvides ordering based on SAM header records' attribute values.Classhtsjdk.samtoolsHtsJDKjavadoc
SamIndexesA helper class to read BAI and CRAI indexes.Classhtsjdk.samtoolsHtsJDKjavadoc
SamInputResourceDescribes a SAM-like resource, including its data (where the records are), and optionally an index.Classhtsjdk.samtoolsHtsJDKjavadoc
SAMLineParserthis class enables creation of a SAMRecord object from a String in SAM text format.Classhtsjdk.samtoolsHtsJDKjavadoc
SamLocusIteratorIterator that traverses a SAM File, accumulating information on a per-locus basis.Classhtsjdk.samtools.utilHtsJDKjavadoc
SamPairUtilClasshtsjdk.samtoolsHtsJDKjavadoc
SAMProgramRecordIn-memory representation of @PG SAM header record.Classhtsjdk.samtoolsHtsJDKjavadoc
SamReaderDescribes functionality for objects that produce SAMRecords and associated information.Interfacehtsjdk.samtoolsHtsJDKjavadoc
SamReaderFactoryDescribes the functionality for producing SamReader, and offers a handful of static generators.Classhtsjdk.samtoolsHtsJDKjavadoc
SAMReadGroupRecordHeader information about a read group.Classhtsjdk.samtoolsHtsJDKjavadoc
SAMRecordJava binding for a SAM file record.Classhtsjdk.samtoolsHtsJDKjavadoc
SAMRecordComparatorInterface for comparators that define the various SAM sort orders.Interfacehtsjdk.samtoolsHtsJDKjavadoc
SAMRecordCoordinateComparatorComparator for sorting SAMRecords by coordinate.Classhtsjdk.samtoolsHtsJDKjavadoc
SAMRecordDuplicateComparatorCompares records based on if they should be considered PCR Duplicates (see MarkDuplicates).Classhtsjdk.samtoolsHtsJDKjavadoc
SAMRecordFactoryFactory interface which allows plugging in of different classes for generating instances of SAMRecord and BAMRecord when reading from SAM/BAM files.Interfacehtsjdk.samtoolsHtsJDKjavadoc
SamRecordFilterAPI for filtering SAMRecordsDetermines whether a SAMRecord matches this filterInterfacehtsjdk.samtools.filterHtsJDKjavadoc
SamRecordIntervalIteratorFactoryCreate an iterator over a SAMFileReader that only returns reads that overlap one of the intervals in an interval list.Classhtsjdk.samtools.utilHtsJDKjavadoc
SAMRecordIteratorA general interface that adds functionality to a CloseableIterator of SAMRecords.Interfacehtsjdk.samtoolsHtsJDKjavadoc
SAMRecordQueryHashComparatorSAMRecord comparator that provides an ordering based on a hash of the queryname.Classhtsjdk.samtoolsHtsJDKjavadoc
SAMRecordQueryNameComparatorComparator for "queryname" ordering of SAMRecords.Classhtsjdk.samtoolsHtsJDKjavadoc
SAMRecordSetBuilderFactory class for creating SAMRecords for testing purposes.Classhtsjdk.samtoolsHtsJDKjavadoc
SamRecordTrackingBufferThis class stores SAMRecords for return.Classhtsjdk.samtools.utilHtsJDKjavadoc
SAMRecordUtilClasshtsjdk.samtoolsHtsJDKjavadoc

Subscribe to Java News and Posts. Get latest updates and posts on Java from Buggybread.com
Enter your email address:
Delivered by FeedBurner

SamRecordWithOrdinalA little class to store the unique index associated with this record.Classhtsjdk.samtools.utilHtsJDKjavadoc
SAMSequenceDictionaryCollection of SAMSequenceRecords.Classhtsjdk.samtoolsHtsJDKjavadoc
Check Code Snippets / Samples for htsjdk.samtools.SAMSequenceDictionary
SAMSequenceDictionaryExtractorTiny class for automatically loading a SAMSequenceDictionary given a fileAuthor:farjoun on 2/25/2014Classhtsjdk.variant.utilsHtsJDKjavadoc
SAMSequenceRecordHeader information about a reference sequence.Classhtsjdk.samtoolsHtsJDKjavadoc
SAMSortOrderCheckerEncapsulates simple check for SAMRecord order.Classhtsjdk.samtoolsHtsJDKjavadoc
SamStreamsClasshtsjdk.samtoolsHtsJDKjavadoc
SAMTagThe standard tags for a SAM record that are defined in the SAM spec.Classhtsjdk.samtoolsHtsJDKjavadoc
SAMTagUtilFacility for converting between String and short representation of a SAM tag.Classhtsjdk.samtoolsHtsJDKjavadoc
SAMTestUtilMisc methods for SAM-related unit tests.Classhtsjdk.samtoolsHtsJDKjavadoc
SAMTextHeaderCodecParser for a SAM text header, and a generator of SAM text header.Classhtsjdk.samtoolsHtsJDKjavadoc
SAMTextWriterWriter for text-format SAM files.Classhtsjdk.samtoolsHtsJDKjavadoc
SAMToolsCommand line utility for manipulating SAM/BAM files.Classhtsjdk.samtoolsHtsJDKjavadoc
SAMUtilsClasshtsjdk.samtoolsHtsJDKjavadoc
SAMValidationErrorClass that encapsulates a validation error message as well as a type code so that errors can be aggregated by type.Classhtsjdk.samtoolsHtsJDKjavadoc
ScoresA read feature representing a contiguous stretch of quality scores in a read.Classhtsjdk.samtools.cram.encoding.readfeaturesHtsJDKjavadoc
SecondaryAlignmentFilterSamRecordFilter that filters out secondary alignments, but not supplemental alignments.Classhtsjdk.samtools.filterHtsJDKjavadoc
SecondaryOrSupplementaryFilterFilter out SAMRecords with NotPrimaryAlignment or Supplementary flag set This class should be viewed as a replacement for NotPrimarySkippingIterator,Classhtsjdk.samtools.filterHtsJDKjavadoc
SecondaryOrSupplementarySkippingIteratorWrapper around SAMRecord iterator that skips over secondary and supplementary elements.Classhtsjdk.samtoolsHtsJDKjavadoc
SeekableBufferedStreamA wrapper class to provide buffered read access to a SeekableStream.Classhtsjdk.samtools.seekablestreamHtsJDKjavadoc
SeekableFileStreamClasshtsjdk.samtools.seekablestreamHtsJDKjavadoc
SeekableFTPStreamUnfortunately the seekable stream classes exist for both Tribble and Picard, and we need both.Classhtsjdk.samtools.seekablestreamHtsJDKjavadoc
SeekableFTPStreamHelperClasshtsjdk.samtools.seekablestreamHtsJDKjavadoc
SeekableHTTPStreamClasshtsjdk.samtools.seekablestreamHtsJDKjavadoc
SeekableMemoryStreamClasshtsjdk.samtools.seekablestreamHtsJDKjavadoc
SeekableStreamClasshtsjdk.samtools.seekablestreamHtsJDKjavadoc

Subscribe to Java News and Posts. Get latest updates and posts on Java from Buggybread.com
Enter your email address:
Delivered by FeedBurner

SeekableStreamFactorySingleton class for getting SeekableStreams from URL/paths Applications using this library can set their own factoryClasshtsjdk.samtools.seekablestreamHtsJDKjavadoc
SequenceUtilClasshtsjdk.samtools.utilHtsJDKjavadoc
SimpleBEDFeatureFeature from a BED file without exon blocks.Classhtsjdk.tribble.bedHtsJDKjavadoc
SimpleFeatureA simple concrete Feature.Classhtsjdk.tribbleHtsJDKjavadoc
SliceCRAM slice is a logical union of blocks into for example alignment slices.Classhtsjdk.samtools.cram.structureHtsJDKjavadoc
SnappyLoaderIf Snappy is available, obtain single-arg ctors for SnappyInputStream and SnappyOutputStream.Classhtsjdk.samtools.utilHtsJDKjavadoc
SnpFilterA Predicate on VariantContexts that returns true at sites that are SNPsAuthor:Yossi FarjounClasshtsjdk.variant.variantcontext.filterHtsJDKjavadoc
SoftClipA read feature representing a soft clip similar to CigarOperator.Classhtsjdk.samtools.cram.encoding.readfeaturesHtsJDKjavadoc
SolexaNoiseFilterFilter to determine whether a read is "noisy" due to a poly-A run that is a sequencing artifact.Classhtsjdk.samtools.filterHtsJDKjavadoc
SolexaQualityConverterOptimized method for converting Solexa ASCII qualities into Phred scores.Classhtsjdk.samtools.utilHtsJDKjavadoc
SortingCollectionCollection to which many records can be added.Classhtsjdk.samtools.utilHtsJDKjavadoc
SortingLongCollectionAccumulate a list of longs that can then be sorted in natural order and iterated over.Classhtsjdk.samtools.utilHtsJDKjavadoc
SortingVariantContextWriterClasshtsjdk.variant.variantcontext.writerHtsJDKjavadoc
SQTagUtilUtility methods for encoding and decoding the SQ tag value of SAMRecord.Classhtsjdk.samtoolsHtsJDKjavadoc
SRAAccessionDescribes a single SRA accession for SRA read collection Also provides app string functionality and allows to check if working SRA is supported on the running platformClasshtsjdk.samtools.sraHtsJDKjavadoc
SRAAlignmentIteratorIterator for aligned reads.Classhtsjdk.samtools.sraHtsJDKjavadoc
SRAFileReaderClasshtsjdk.samtoolsHtsJDKjavadoc
SRAIndexEmulates BAM index so that we can request chunks of records from SRAFileReader Here is how it works:Classhtsjdk.samtoolsHtsJDKjavadoc
SRAIndexedSequenceFileClasshtsjdk.samtools.sraHtsJDKjavadoc
SRAIteratorClasshtsjdk.samtoolsHtsJDKjavadoc
SRALazyRecord Since SRA is a column oriented database, it is very inefficient to load all the fields at once.Classhtsjdk.samtools.sraHtsJDKjavadoc
SRAUnalignmentIteratorIterator for unaligned reads.Classhtsjdk.samtools.sraHtsJDKjavadoc
SRAUtilsProvides some functionality which can be used by other classes Created by andrii.Classhtsjdk.samtools.sraHtsJDKjavadoc
StopWatchUtility to help in performance testing.Classhtsjdk.samtools.utilHtsJDKjavadoc
StrandEnum for strand, which can be encoded as stringEnum Constant SummaryClasshtsjdk.tribble.annotationHtsJDKjavadoc

Subscribe to Java News and Posts. Get latest updates and posts on Java from Buggybread.com
Enter your email address:
Delivered by FeedBurner

StringHeaderA simple header who's data type is a single String.Classhtsjdk.samtools.metricsHtsJDKjavadoc
StringLineReader is necessary because the String is in unicode.Classhtsjdk.samtools.utilHtsJDKjavadoc
StringUtilGrab-bag of stateless String-oriented utilities.Classhtsjdk.samtools.utilHtsJDKjavadoc
SubexponentialIntegerEncodingClasshtsjdk.samtools.cram.encodingHtsJDKjavadoc
SubstitutionA substitution event captured in read coordinates.Classhtsjdk.samtools.cram.encoding.readfeaturesHtsJDKjavadoc
SubstitutionMatrixClasshtsjdk.samtools.cram.structureHtsJDKjavadoc
TabixFeatureReaderClasshtsjdk.tribbleHtsJDKjavadoc
TabixFormatThe values in a Tabix header that define the format of the file being indexed, e.Classhtsjdk.tribble.index.tabixHtsJDKjavadoc
TabixIndexThis class represent a Tabix index that has been built in memory or read from a file.Classhtsjdk.tribble.index.tabixHtsJDKjavadoc
TabixIndexCreatorIndexCreator for Tabix.Classhtsjdk.tribble.index.tabixHtsJDKjavadoc
TabixIteratorLineReaderClasshtsjdk.tribble.readersHtsJDKjavadoc
TabixReaderClasshtsjdk.tribble.readersHtsJDKjavadoc
TabixUtilsClasshtsjdk.tribble.utilHtsJDKjavadoc
TagFilterClasshtsjdk.samtools.filterHtsJDKjavadoc
TagValueAndUnsignedArrayFlagCVO to use as a method return value.Classhtsjdk.samtoolsHtsJDKjavadoc
TempStreamFactoryFactory class for wrapping input and output streams for temporary files.Classhtsjdk.samtools.utilHtsJDKjavadoc
TestUtilClasshtsjdk.samtools.utilHtsJDKjavadoc
TextCigarCodecConvert between String and Cigar class representations of CIGAR.Classhtsjdk.samtoolsHtsJDKjavadoc
TextTagCodecConverter between SAM text representation of a tag, and in-memory Object representation.Classhtsjdk.samtoolsHtsJDKjavadoc
TimeChannelClasshtsjdk.samtools.appsHtsJDKjavadoc
TimeRandomAccessFileClasshtsjdk.samtools.appsHtsJDKjavadoc
TribbleClasshtsjdk.tribbleHtsJDKjavadoc
TribbleExceptionClasshtsjdk.tribbleHtsJDKjavadoc
TribbleIndexCreatorBase class for Tribble-specific index creators.Classhtsjdk.tribble.indexHtsJDKjavadoc
TribbleIndexedFeatureReaderA reader for text feature files (i.Classhtsjdk.tribbleHtsJDKjavadoc

Subscribe to Java News and Posts. Get latest updates and posts on Java from Buggybread.com
Enter your email address:
Delivered by FeedBurner

TrimmingUtilUtility code for performing quality trimming.Classhtsjdk.samtools.utilHtsJDKjavadoc
TupleA simple tuple class.Classhtsjdk.samtools.utilHtsJDKjavadoc
UnsortedFileExceptionan exception for when we've discovered that an input file is unsorted; sorted files are required by TribbleSee Also:Serialized FormClasshtsjdk.tribble.exceptionHtsJDKjavadoc
URLHelperInterface defining a helper class for dealing with URL resources.Interfacehtsjdk.tribble.utilHtsJDKjavadoc
UserPasswordInputInterfacehtsjdk.samtools.seekablestreamHtsJDKjavadoc
ValidationStringencyenum ValidationStringencyHow strict to be when reading a SAM or BAM, beyond bare minimum validation.Classhtsjdk.samtoolsHtsJDKjavadoc
VariantContext High-level overview The VariantContext object is a single general class system for representing genetic variation data composed of:Classhtsjdk.variant.variantcontextHtsJDKjavadoc
VariantContextBuilderBuilder class for VariantContext.Classhtsjdk.variant.variantcontextHtsJDKjavadoc
VariantContextComparatorA Comparator that orders VariantContexts by the ordering of the contigs/chromosomes in the List provided at construction time, then by start position with each contig/chromosome.Classhtsjdk.variant.variantcontextHtsJDKjavadoc
VariantContextFilterAPI for filtering VariantContextsAuthor:Yossi FarjounInterfacehtsjdk.variant.variantcontext.filterHtsJDKjavadoc
VariantContextUtilsClasshtsjdk.variant.variantcontextHtsJDKjavadoc
VariantContextWriterthis class writes VCF filesattempt to close the VCF fileInterfacehtsjdk.variant.variantcontext.writerHtsJDKjavadoc
VariantContextWriterBuilder Provides methods for creating VariantContextWriters using the Builder pattern.Classhtsjdk.variant.variantcontext.writerHtsJDKjavadoc
VariantContextWriterFactoryFactory methods to create VariantContext writersSince:5/12Author:depristoClasshtsjdk.variant.variantcontext.writerHtsJDKjavadoc
VCF3CodecA feature codec for the VCF3 specification, to read older VCF files.Classhtsjdk.variant.vcfHtsJDKjavadoc
VCFCodecA feature codec for the VCF 4 specification VCF is a text file format (most likely stored in a compressed manner).Classhtsjdk.variant.vcfHtsJDKjavadoc
VCFCompoundHeaderLinea base class for compound header lines, which include info lines and format lines (so far)See Also:Serialized FormClasshtsjdk.variant.vcfHtsJDKjavadoc
VCFConstantsClasshtsjdk.variant.vcfHtsJDKjavadoc
VCFContigHeaderLineA special class representing a contig VCF header line.Classhtsjdk.variant.vcfHtsJDKjavadoc
VCFEncoderFunctions specific to encoding VCF records.Classhtsjdk.variant.vcfHtsJDKjavadoc
VCFFileReaderSimplified interface for reading from VCF/BCF files.Classhtsjdk.variant.vcfHtsJDKjavadoc
VCFFilterHeaderLineClasshtsjdk.variant.vcfHtsJDKjavadoc
VCFFormatHeaderLine Class VCFFormatHeaderLine A class representing a key=value entry for genotype FORMAT fields in the VCF headerSee Also:Serialized FormClasshtsjdk.variant.vcfHtsJDKjavadoc
VCFHeaderA class to represent a VCF header NOTE: This class stores header lines in lots of places.Classhtsjdk.variant.vcfHtsJDKjavadoc
VCFHeaderLine Class VCFHeaderLine A class representing a key=value entry in the VCF headerClasshtsjdk.variant.vcfHtsJDKjavadoc

Subscribe to Java News and Posts. Get latest updates and posts on Java from Buggybread.com
Enter your email address:
Delivered by FeedBurner

VCFHeaderLineCountenum VCFHeaderLineCountthe count encodings we use for fields in VCF header linesClasshtsjdk.variant.vcfHtsJDKjavadoc
VCFHeaderLineTranslatorClasshtsjdk.variant.vcfHtsJDKjavadoc
VCFHeaderLineTypeenum VCFHeaderLineTypethe type encodings we use for fields in VCF header linesClasshtsjdk.variant.vcfHtsJDKjavadoc
VCFHeaderVersionenum VCFHeaderVersioninformation that identifies each header versionClasshtsjdk.variant.vcfHtsJDKjavadoc
VCFIDHeaderLineInterfacehtsjdk.variant.vcfHtsJDKjavadoc
VCFInfoHeaderLine Class VCFInfoHeaderLine A class representing a key=value entry for INFO fields in the VCF headerClasshtsjdk.variant.vcfHtsJDKjavadoc
VCFRecordCodecWrites VariantContext instances to an OutputStream without headers or metadata.Classhtsjdk.variant.vcfHtsJDKjavadoc
VCFSimpleHeaderLineClasshtsjdk.variant.vcfHtsJDKjavadoc
VCFStandardHeaderLinesManages header lines for standard VCF INFO and FORMAT fields.Classhtsjdk.variant.vcfHtsJDKjavadoc
VCFUtilsClasshtsjdk.variant.vcfHtsJDKjavadoc
VersionA class to represent a version information, 3 number: major, minor and build number.Classhtsjdk.samtools.cram.commonHtsJDKjavadoc
VersionHeaderHeader that stores information about the version of some piece of software or data used to create the metrics file.Classhtsjdk.samtools.metricsHtsJDKjavadoc
WholeGenomeReferenceSequenceMaskClasshtsjdk.samtools.utilHtsJDKjavadoc
WholeReadClippedFilterFilter SAMRecords so that only those that have at least one un-clipped base areAuthor:ktibbett@broadinstitute.Classhtsjdk.samtools.filterHtsJDKjavadoc
WriterClasshtsjdk.samtools.cram.encoding.writerHtsJDKjavadoc

Subscribe to Java News and Posts. Get latest updates and posts on Java from Buggybread.com
Enter your email address:
Delivered by FeedBurner



comments powered by Disqus